tbuckley/cabot-search huggingface dataset:
Abstract 3889: Identification of ADRN-specific, MES-specific, and pan-subtype therapeutic targets in neuroblastoma
Authors: Nathan M. Kendsersky, Nathaniel W. Mabe, Alvin Farrel, Liron D. Grossmann, Michal Odrobina, Kimberly Stegmaier, John M. Maris
Journal: Cancer Research (2022)

Abstract Background: Neuroblastoma is an extracranial solid tumor of childhood that arises from the developing sympathetic nervous system. Half of patients with high-risk disease do not survive despite multimodal therapy, and survival after relapse is unlikely. Recent studies have characterized two distinct neuroblastoma cell subtypes: the adrenergic (ADRN) subtype of sympathetic noradrenergic-like identity and the mesenchymal (MES) subtype of neural crest-like identity. ADRN-like cells are more aggressive and proliferative, while the MES-like cells are chemotherapy resistant. Neuroblastoma tumors are heterogenous and comprised of both ADRN and MES cell subtypes, which likely leads to differential responses to therapy. Thus, to eliminate cells that may lead to tumor relapse, it is critical to develop therapies against both neuroblastoma subtypes. Methods: To identify candidate subtype-specific therapeutic targets, we used ssGSEA to classify human neuroblastoma tumors into ADRN- or MES-dominant and performed differential expression. We validated subtype-specific targets in additional datasets and models, including transdifferentiated neuroblastoma cell lines (ADRN-to-MES) after inducible overexpression of the MES transcription factor PRRX1. Results: We show ADRN-specific expression of known preclinical and clinical neuroblastoma targets with limited or no expression in MES-dominant tumors. We propose CD276 (B7-H3) and L1CAM as pan-subtype targets with similar expression in both subtypes and stable expression after ADRN-to-MES transdifferentiation. In MES-specific neuroblastoma patient samples and cell lines, we identify the receptor tyrosine kinase AXL as a candidate MES target. MES neuroblastoma cell lines are more sensitive to small molecule AXL inhibitors (Cabozantinib, NPS-1034, and ONO-7475) compared to ADRN cell lines. We also observe higher expression of PDL1 and immunosuppressive chemokines in MES-dominant tumors and cell lines. Finally, we detect AXL and Gas6 transcripts in tumor-resident macrophages and fibroblasts, which may further promote immune evasion. Conclusion: Here we have identified and prioritized ADRN-specific, MES-specific, and pan-subtype neuroblastoma therapeutic targets and suggest AXL-targeted therapy may eliminate both MES-dominant neuroblastoma cells and immune cell populations that contribute to an immunosuppressive microenvironment. Citation Format: Nathan M. Kendsersky, Nathaniel W. Mabe, Alvin Farrel, Liron D. Grossmann, Michal Odrobina, Kimberly Stegmaier, John M. Maris. Identification of ADRN-specific, MES-specific, and pan-subtype therapeutic targets in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3889.
Abstract 3203: Cutting edge biomarkers strategy to provide early insights into activity of EVT-801, a novel selective VEGFR-3 inhibitor that targets tumor angiogenesis during the FIH clinical trial
Authors: Michael R. Paillasse, James Garner, Michael Fitzgerald, Lise Davenne, Pierre-Benoit Ancey, celine Poussereau-Pomie, Michael Esquerre, Gaelle Badet, Joel Tuyaret, Marie Mandron, Philippe Rochaix, Maha Ayyoub, Clara Maria Scarlata, Christine Ménétrier-Caux, Chrsitophe CAUX, Philippe Cassier, Jean-Pierre Delord, Carlos Gomez Roca, Pierre Fons
Journal: Cancer Research (2022)

Abstract Introduction: EVT801 is a highly selective small molecule inhibitor of VEGFR3 and acts by inhibiting lymphangiogenesis and tumor angiogenesis in and around the tumor. It has shown compelling activity in a wide range of cancer models and is well-tolerated in preclinical toxicology studies. A phase I study is underway and will focus primarily on understanding the safety, tolerability, and pharmacokinetics of EVT801 across a range of doses. Methods: The first stage of the study is designed to determine the maximum tolerated dose (MTD) and recommended Phase II dose (RP2D) for EVT801, with a second stage aiming to confirm RP2D in selected cancer patient populations. Clinical samples from these patients will be used to explore preliminary signals of clinical efficacy and investigate the biological activity of the drug using several biomarkers. Efficacy biomarkers will include imaging approaches (DCE-MRI and CEUS) to characterize tumor vascularization, as well as analysis of protein and mRNA quantification in on-treatment biopsies vs pre-treatment biopsies. Moreover, the relationship between activity of EVT801 and expression of key markers at protein and mRNA level will be investigated to potentially establish biomarkers for patient stratification and selection. Lastly, target engagement and pharmacodynamics effects will be investigated by immuno-monitoring as well as assessment of a defined set of proteins as markers of inflammation and angiogenesis as identified in preclinical in vivo models. We expect that these analyses will help to better understand the effects of the drug in human subjects and may also help to select the most responsive patients and provide early signs of clinical efficacy. Citation Format: Michael R. Paillasse, James Garner, Michael Fitzgerald, Lise Davenne, Pierre-Benoit Ancey, celine Poussereau-Pomie, Michael Esquerre, Gaelle Badet, Joel Tuyaret, Marie Mandron, Philippe Rochaix, Maha Ayyoub, Clara Maria Scarlata, Christine Ménétrier-Caux, Chrsitophe CAUX, Philippe Cassier, Jean-Pierre Delord, Carlos Gomez Roca, Pierre Fons. Cutting edge biomarkers strategy to provide early insights into activity of EVT-801, a novel selective VEGFR-3 inhibitor that targets tumor angiogenesis during the FIH clinical trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3203.
Abstract 5101: Urine based dynamically monitoring reflect pathologic response in MIBC patients with neoadjuvant immunotherapy
Authors: Xiao Yang, Lingkai Cai, Qiang Cao, Min Shi, Yiming Liang, Yurong Qu, Qiang Lu
Journal: Cancer Research (2022)

Abstract Background: The recommended standard of care treatment for nonmetastatic muscle-invasive bladder cancer (MIBC) is radical cystectomy (RC). Even with urinary diversion, radical cystectomy has a major impact on patients' quality of life. Although high rates of overall and disease-specific survival were observed in patients managed with bladder preservation, who achieved a clinically complete response to neoadjuvant therapy. Frequent evaluation of tumor response based cystoscopy implementing personalized bladder-sparing treatment paradigms. Case Presentation: Here, we report on a case of urine-based dynamically monitoring during neoadjuvant immunotherapy in a MIBC patient treated with RC. A 57-year-old male presented macrohematuria and was diagnosed with bladder urothelial carcinoma by transurethral resection of bladder tumor (TURBT) with clinical stage IIIA (high-grade, multiple, cT2N0M0). He received 3 cycles of Tislelizumab monotherapy and sequential radical cystectomy. The RC specimen showed a complete pathological response (pCR). Four urine samples were collected prior to TURBT, on a day after TURBT, at beginning of neoadjuvant immunotherapy, and on the day of CR. Mutations status in 17 genes and methylation level of ONECUT2 were analyzed by a high-throughput sequencing-based urine test panel (genetron-uro-V1). In urine sediment DNA, which was collected before TURBT, the TERT promoter mutations C228T, TP53 D281H, and ERBB2 D277Y were detected in urine sediment DNA at variant allele frequencies (VAF) of 31.8%, 10.5%, and 0.5%, respectively. After removing in most parts of tumor, the VAF of TERT C228T decreased to 19.6% and mutation in TP53 and ERBB2 could not be detected. Without neoadjuvant immunotherapy, the VAF of TERT C228T still stayed above 12%. After 3 cycles of Tislelizumab monotherapy on the day of CR, all mutation was below the detection limit in urine sediment DNA, which was consistent with pCR in the pathological report of RC specimen. Conclusions: This case suggested that urine-based dynamically monitoring reflected pathologic response, which could support personalized care and help select patients for bladder-sparing treatment. Citation Format: Xiao Yang, Lingkai Cai, Qiang Cao, Min Shi, Yiming Liang, Yurong Qu, Qiang Lu. Urine based dynamically monitoring reflect pathologic response in MIBC patients with neoadjuvant immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5101.
Abstract 5825: Reduced miR-371b-5p expression drives tumor progression via CSDE1/RAC1 regulation in triple-negative breast cancer
Authors: Jong Hoon Park, Yesol Kim, Je Yeong Ko, Soo-Been Lee, Minah Park
Journal: Cancer Research (2022)

Abstract Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer; however, specific prognostic biomarkers have not yet been developed. In this study, we identified dysregulated microRNAs (miRNAs) in TNBC by profiling miRNA and mRNA expression. In patients with TNBC, miR-371b-5p expression was reduced, and miR-371b-5p overexpression significantly mitigated TNBC cell growth, migration, and invasion. In addition, we found that expression of cold shock domain-containing protein E1 (CSDE1), a direct target gene of miR-371b-5p, was upregulated in TNBC cells, and inhibition of CSDE1 expression alleviated TNBC cell growth by regulating RAC1 transcription. Mechanistically, CSDE1, phosphorylated C-terminal domain (p-CTD) of RNA polymerase II (RNAPII), and CDK7 form a complex, and downregulation of CSDE1 leads to weak interaction between RNAPII p-CTD and CDK7, resulting in a decrease in RNAPII p-CTD expression to reduce RAC1 transcript levels in CSDE1-deficient TNBC cells. Our data demonstrate that miR-371b-5p is a tumor-suppressive miRNA that regulates the CSDE1/Rac1 axis and could be a potential prognostic biomarker for TNBC. Citation Format: Jong Hoon Park, Yesol Kim, Je Yeong Ko, Soo-Been Lee, Minah Park. Reduced miR-371b-5p expression drives tumor progression via CSDE1/RAC1 regulation in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5825.
Abstract LB161: Whole mammogram image improves breast cancer prediction
Authors: Shu Jiang, Graham A. Colditz
Journal: Cancer Research (2022)

Abstract To efficiently capture data from mammographic breast images and classify long term risk of breast cancer, we developed methods that use the extensive existing data that are currently ignored in the context of breast cancer risk stratification. More than 20 studies support texture features add value to risk prediction beyond breast density. However, the entire mammogram imaging data has a high dimension of pixels (~13 million per image), greatly exceeding the number of women in a cohort. We apply functional principal component analysis methods to predict 5-years breast cancer incidence using baseline mammograms. We applied these methods onto women participating in the Joanne Knight Breast Health Cohort which is comprised of over 10,000 women undergoing repeated mammography screening at Siteman Cancer Center and followed since 2010. All women had baseline mammogram at entry, provided a blood sample and completed a risk factor questionnaire. Mammograms are all using the same technology (Hologic). During follow-up through October 2020, we identified 246 incident breast cancer cases (pathology confirmed) and matched them to controls from the perspective cohort based on month of mammogram and age at entry. In a baseline model we controlled for age, menopause, BMI, and mammographic breast density (BIRADs). We then added the full image (characterized by the FPC) to the base model and further compared the AUC of the new model vs the base model using the likelihood ratio test. AUC is validated with internal 10-fold cross validation. The AUC for 5-year breast cancer risk classification increased significantly from a median of 0.61 (sd 0.09 for estimated AUCs across 10-fold internal validation) for the baseline model to 0.70 (0.10) when the full image is added, p &amp;lt; 0.001. We conclude that using full mammogram images for breast cancer risk prediction captures additional information on breast tissue characteristics that relate to cancer risk, and improves prediction classification. This prediction algorithm can run efficiently in real time (in seconds) with processing of digital mammograms. Thus, this model can be easily implemented in mammography screening services and other clinical settings to guide real-time risk stratification to improve precision prevention of the leading cancer in women world-wide. Further analysis will quantify the value of adding other breast cancer risk factors, including polygenic risk scores. Addition of repeated mammogram images over time should further increase classification performance. This approach has the potential to improve risk classification by using data already available for the vast majority of women already having repeated screening mammograms. Citation Format: Shu Jiang, Graham A. Colditz. Whole mammogram image improves breast cancer prediction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB161.
Abstract 5420: DPYD enhancer variant confers increased risk of severe toxicity in 5-FU chemotherapy
Authors: Ting Zhang, Alisa Ambrodji, Huixing Huang, Kelly Bouchonville, Amy Etheridge, Remington Schmidt, Jose Cardiel Nunez, Zoey Temesgen, Federico Innocenti, Robert Diasio, Carlo Largiadèr, Steven M. Offer
Journal: Cancer Research (2022)

Abstract Genetic variants in the DPYD gene that are deleterious to dihydropyrimidine dehydrogenase (DPD) enzyme function have demonstrated clinical validity as predictive biomarkers for severe (i.e., CTCAE grade ≥3) and potentially lethal toxicity to fluorouracil (5-FU) and capecitabine chemotherapies. Variants within the coding region only explain 5-10% of 5-FU-related toxicities; and GWAS approaches have been unable to identify validated predictive biomarkers to date. Our previous studies demonstrated that DPD expression was controlled by multiple epigenetic processes; considerable variation was also noted in liver DPYD/DPD levels. Using CRISPR-interference (CRISPRi) and CRISPR-activation (CRISPRa), we identified functional enhancer regions within liver tissues and cells. Epigenetic status at these regions was shown to correlate with DPYD expression in cell models and human liver tissues. Chromosome conformation capture (3C) confirmed direct promoter-enhancer interactions. A multi-omics analysis of &amp;gt;1000 human liver specimens identified a proximal eQTL for DPYD expression within an enhancer, with a global minor allele frequency of 27%. This variant was subsequently shown to directly alter DPYD expression in knock-in cell line models. The variant disrupts transcription factor binding at the DPYD enhancer, leading to reduced enhancer-promoter interaction, reduced DPD expression, and increased cellular sensitivity to 5-FU. Collectively, our data suggest that the variant could represent a novel predictive biomarker for severe 5-FU toxicity. The evaluation of this marker in the clinical setting is currently underway. Citation Format: Ting Zhang, Alisa Ambrodji, Huixing Huang, Kelly Bouchonville, Amy Etheridge, Remington Schmidt, Jose Cardiel Nunez, Zoey Temesgen, Federico Innocenti, Robert Diasio, Carlo Largiadèr, Steven M. Offer. DPYD enhancer variant confers increased risk of severe toxicity in 5-FU chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5420.
Abstract 5123: Establishing circulating tumor cell-derived xenografts following a period of <i>in vitro</i> culture
Authors: Jerry Xiao, Richard Schlegel, Seema Agarwal
Journal: Cancer Research (2022)

Abstract Cancer metastasis—the spread of cancer cells from a primary node to a distant site—is responsible for as much as 90% of all cancer-associated deaths due to treatment resistance and increased tumor burden. Once established, metastatic nodules oftentimes exhibit distinct molecular phenotypes from their original primary tumor, undermining gold-standard methods for determining treatments for patients, which typically rely on molecular characterization of the primary tumor. Unfortunately, a lack of robust, scalable, and appropriate models for studying differences in patient-derived primary and metastatic tumors has hindered progress in identifying metastasis-specific therapies. Previously, we reported the ability to establish in vitro cultures of circulating tumor cells (CTCs), a unique precursor population of cells that exhibits an ability to escape the primary tumor but not yet fully complete metastasis. We have since expanded the application of this GU-CTC platform to culture CTCs from the blood of patients diagnosed with a variety of metastatic cancers, resulting in the successful culture of 31 unique patient-derived CTC cell lines. Furthermore, following an initial short-term culture period, we also performed subcutaneous injection of mixed CTC cultures into immunocompromised mice, resulting in not only primary tumor formation, but also systemic metastatic nodule formation in as short as 3 months. These resulting CTC-derived xenografts (CDXs) have been demonstrated using metastatic pancreatic, colorectal, and lung adenocarcinoma-derived CTCs. Encouragingly, all CDX models also exhibited replicable metastatic patterns upon reimplantation, reinforcing the important role of CTCs as precursors to metastasis. Bulk RNA-sequencing of patient-matched whole blood, cultured CTCs, and CDX-derived primary tumor and metastatic tissues further identified enrichment of an epithelial-mesenchymal transition as well as several cancer-specific gene signatures consistent with an invasive phenotype. This extended GU-CTC platform therefore enables not only the robust and rapid expansion of CTCs through both in vitro and in vivo methods, but also offers an avenue for personalized drug screens in the effort to target cancer metastasis. Citation Format: Jerry Xiao, Richard Schlegel, Seema Agarwal. Establishing circulating tumor cell-derived xenografts following a period of in vitro culture [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5123.
Abstract 5750: Quantification of histone methylation regulator-associated modification patterns was a potential biomarker for prognosis and associated with immunotherapy in gastric cancer
Authors: Jiapeng Kang, Lu Yang, Jialin Lin, Dan Zhou, Canbin Fang, Feng Ye, Weiwei Tang
Journal: Cancer Research (2022)

Abstract Background: Histone methylation (HM) is an abundant form of histone modification and recent studies have highlighted it strongly related to tumorigenicity and progression. However, histone methylation modification patterns and potential roles in gastric cancer have not been systematically elucidated. Method: In this study, we curated 53 histone methyltransferase regulators and 9 histone demethylase regulators. Identified histone methylation(HM)modification clusters based on the expression of 62 HM regulators. Principal component analysis (PCA) served to construct histone methylation score (HMScore) base on differential genes among three HM clusters. Evaluating the relationship between HMScore and clinical prognosis, tumor mutation burden (TMB), microsatellite instability (MSI), immune cell infiltration and immunotherapy. Results: We identified distinct three HM modification clusters in patients with gastric cancer based on the expression of 62 HM regulators, which were association with different clinical prognosis, biological pathways and tumor microenvironment characterization. Based on HMScore to quantitatively evaluate the histone methylation modification patterns in gastric cancer patients. We founded that patients with a low-HMScore group(score&amp;lt;2.276) was association with poor prognosis. In addition, high-HMScore group(score≥2.276) displayed tumor mutation burden-high (TMB-H) and microsatellite instability-high (MSI-H), and correlation analysis indicated that HMScore was positively correlated with tumor mutation burden. Immune infiltration correlation analysis showed that HMScore strongly negative related to MDSC cell, mast cell and regulatory T cell. Survival analysis indicated that patients with TMB-H and high-HMScore were related to long clinical prognosis in gastric cancer. Moreover, patients with high-HMScore group had high abundance of PD-L1, and high-HMScore was confirmed sensitive response to immunotherapy in gastric cancer. Conclusion: This study provided a new model to evaluate individual gastric cancer histone methylation modification patterns. HMScore was benefit to evaluate clinical prognosis value and guide strategies to improve treatment in gastric cancer. Citation Format: Jiapeng Kang, Lu Yang, Jialin Lin, Dan Zhou, Canbin Fang, Feng Ye, Weiwei Tang. Quantification of histone methylation regulator-associated modification patterns was a potential biomarker for prognosis and associated with immunotherapy in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5750.